www.nature.com/scientificreports OPEN Exploring Cuba’s population structure and demographic history using genome-wide data Received: 9 February 2018 Cesar Fortes-Lima 1, Jonas Bybjerg-Grauholm 2,3, Lilia Caridad Marin-Padrón4, Accepted: 10 July 2018 Enrique Javier Gomez-Cabezas5, Marie Bækvad-Hansen2,3, Christine Søholm Hansen2,3, Published: xx xx xxxx Phuong Le6, David Michael Hougaard 2,3, Paul Verdu1, Ole Mors3,7, Esteban J. Parra6 & Beatriz Marcheco-Teruel4 Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. Here, we take advantage of dense genomic data from 860 Cuban individuals to reconstruct the genetic structure and ancestral origins of this population. We found distinct admixture patterns between and within the Cuban provinces. Eastern provinces have higher African and Native American ancestry contributions (average 26% and 10%, respectively) than the rest of the Cuban provinces (average 17% and 5%, respectively). Furthermore, in the Eastern Cuban region, we identifed more intense sex- specifc admixture patterns, strongly biased towards European male and African/Native American female ancestries. Our subcontinental ancestry analyses in Cuba highlight the Iberian population as the best proxy European source population, South American and Mesoamerican populations as the closest Native American ancestral component, and populations from West Central and Central Africa as the best proxy sources of the African ancestral component. Finally, we found complex admixture processes involving two migration pulses from both Native American and African sources. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti. Te islands of the Caribbean were one of the last regions of the Americas to be colonized by anatomically modern humans1. According to archaeological evidence, two groups of hunter-fsher-gatherers associated with diferent cultures (Ortoiroid and Casimiroid), entered the archipelago at diferent times. Te frst group originated from northern South America (Venezuela and Guyana), settled in Trinidad around 6,000 BCE, and then expanded to the north along the Lesser Antilles1,2. Te second group moved around 4,500–4,000 BCE from the Yucatan Peninsula to Hispaniola and Cuba—the largest island of the Greater Antilles1,2. Around 350 BCE, the arrival of Arawak-speaking people from Venezuela, associated with the horticulturalist Saladoid culture, changed the anthropological landscape in the Caribbean, and became the major group3. At the time of the frst contacts with European settlers, Cuba was inhabited by three autochthonous groups: the “Guanahatabey”; the “Ciboney” or “Western Taíno”; and the “Classic Taíno” (living in Western, Central, and Eastern Cuba, respectively)1,3. Late in the ffeenth century, the arrival of Spanish settlers had a profound impact on the indigenous popu- lation of the Caribbean4. Te indigenous Cuban population was decimated during the early colonial period5,6. Te Spanish settlers then started to bring sub-Saharan enslaved Africans7,8. During the transatlantic slave trade (TAST) from 1526 to 1875, approximately 853,000 enslaved Africans were forcibly deported to Cuba9,10. Te vast 1UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l’Homme, Paris, 75016, France. 2Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark. 3The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark. 4National Centre of Medical Genetics, Medical University of Havana, Havana, 10600, Cuba. 5Centre for Sociological and Psychological Research, Havana, 10600, Cuba. 6Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada. 7Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, 8240, Denmark. Cesar Fortes-Lima and Esteban J. Parra contributed equally to this work. Correspondence and requests for materials should be addressed to E.J.P. (email: [email protected]) or B.M.-T. (email: beatriz@ infomed.sld.cu) SCIENTIFIC REPORTS | (2018) 8:11422 | DOI:10.1038/s41598-018-29851-3 1 www.nature.com/scientificreports/ majority (92%) arrived during the last phase of the TAST from 1801 to 187510,11. Te most important embarkation regions were West-Central Africa (30.0% embarked from modern Republic of Congo, Democratic Republic of Congo, and Angola), the Bight of Biafra (26.1% from modern Eastern Nigeria, Cameroon, Equatorial Guinea, and Gabon), the Bight of Benin (14.2% from modern Togo, Benin, and Western Nigeria), Southeast Africa (11.1% from modern Southern Tanzania, Mozambique, and Madagascar), Sierra Leone (9.6% from modern Guinea Bissau, Guinea, and Sierra Leone), the Gold Coast (4.0% from modem Ghana), the Senegambia (3.8% from modern Senegal and Gambia), and the Windward Coast (1.2% from modem Liberia and Ivory Coast)9–11. While broad embarkation regions can be identifed based on historical evidence9,12, the geographical origins of enslaved Africans forcibly displaced during the TAST remain unclear. Troughout the colonial and post-colonial periods, European migrations coming to Cuba primarily origi- nated from diferent regions of the Iberian Peninsula6,12. Te nineteenth century witnessed the arrival of over 125,000 contract workers from China, almost exclusively males (99%), to work in the sugar plantations6,13. Although archaeologists and historians have reconstructed the migratory processes underlying Cuban demo- graphic history, a number of long-standing questions remain unsolved, mostly due to the patchy archaeological and historical records6, and the incomplete and biased information regarding the illegal slave trade12. Previous genetic studies have provided relevant insights into the population history and admixture dynamics in Cuba14–16. Based on a limited set of mitochondrial DNA (mtDNA) and Y-chromosome markers from 254 Cuban individuals, Mendizabal et al.14 highlighted a strong sex-bias in the admixture process, with male lineages mostly tracing to Europe and female lineages to Africa. Cintado et al.15 employed a small panel of seventeen ancestry informative markers (AIMs) to characterize admixture proportions in 206 individuals from Havana— the largest city in Cuba. Marcheco-Teruel et al.16 carried out admixture analyses using around 1,000 individuals from all the ffeen Cuban provinces, and a panel of 128 AIMs as well as diagnostic mtDNA and Y-chromosome markers. Tese authors reported extensive variation in admixture proportions in diferent Cuban regions. Te studies highlighted above were hampered by the relatively small number of genetic markers considered. More recently, Moreno-Estrada et al.17 used genome-wide microarray data to study a diverse set of Caribbean popu- lations, including 80 individuals from Cuba. Tey were able to investigate distinct subcontinental source pop- ulations. Likewise, other recent studies18–20 have employed dense genomic datasets to provide insights into the genetic structure of the Cuban population. However, the sample sizes of these studies were relatively small and did not capture well the demographic composition of the present Cuban population. Additionally, the number of continental reference populations considered in these studies was also quite limited. Here, we substantially expand our previous research16 to explore Cuba’s population structure and demo- graphic history, by using a dense genome-wide SNP dataset of 860 individuals born in Cuba. Importantly, this Cuban sample covers all the ffeen Cuban provinces and is an excellent representation of the current distribu- tion of the Cuban population in terms of sex, age, and population density. Based on both non-parametric and haplotype-based methods, we frst describe genetic diversity patterns in the present-day Cuban population in relation to other worldwide populations, including Hispanic/Latino populations in the Americas. Te inferred distributions of continental ancestries reflect broad-scale geographic admixture patterns across Cuba, and unravel regional diferences within and between Cuban provinces. We then evaluate whether there are difer- ences in patterns of sex-specifc admixture in Cuba. To delve deeper into the founding of the Cuban population, we address hypotheses regarding the Cuban putative ancestral source populations by analysing genetic afnities with populations from specifc regions in Africa, Europe, and the Americas. Furthermore, we address whether gene fow in the Cuban population has been the result of recent multiway migration events involving diferent continental sources. We applied a model-testing approach to infer and reconstruct admixture histories across Cuba in the context of the TAST and afer its abolition. Overall, our research emphasizes fner-scale aspects of genetic diversity patterns in the current Cuban population, provides new insights on the geographical origins of enslaved Africans forced to move to Cuba, and highlights complex demographic histories during and afer the slave trade period. Results Genetic diversity and dissimilarity patterns across Hispanic/Latino populations. To explore inter-individual genetic variation in Cuban and other Hispanic/Latino populations, we frst evaluated allele-shar- ing dissimilarity (ASD)21 across all pairs of individuals in the dataset of Cuban and worldwide